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- PDB-4fbm: LipS and LipT, two metagenome-derived lipolytic enzymes increase ... -

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Basic information

Entry
Database: PDB / ID: 4fbm
TitleLipS and LipT, two metagenome-derived lipolytic enzymes increase the diversity of known lipase and esterase families
ComponentsLipS lipolytic enzyme
KeywordsHYDROLASE / thermostable / Structural Genomics / Enzyme Function Initiative / Structural Proteomics in Europe / SPINE / alpha/beta hydrolases / lipase
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / BROMIDE ION
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChow, J. / Krauss, U. / Dall Antonia, Y. / Fersini, F. / Schmeisser, C. / Schmidt, M. / Menyes, I. / Bornscheuer, U. / Lauinger, B. / Bongen, P. ...Chow, J. / Krauss, U. / Dall Antonia, Y. / Fersini, F. / Schmeisser, C. / Schmidt, M. / Menyes, I. / Bornscheuer, U. / Lauinger, B. / Bongen, P. / Pietruszka, J. / Eckstein, M. / Thum, O. / Liese, A. / Mueller-Dieckmann, J. / Jaeger, K.-E. / Kovavic, F. / Streit, W.R. / Structural Proteomics in Europe (SPINE)
CitationJournal: Plos One / Year: 2012
Title: The Metagenome-Derived Enzymes LipS and LipT Increase the Diversity of Known Lipases.
Authors: Chow, J. / Kovacic, F. / Dall Antonia, Y. / Krauss, U. / Fersini, F. / Schmeisser, C. / Lauinger, B. / Bongen, P. / Pietruszka, J. / Schmidt, M. / Menyes, I. / Bornscheuer, U.T. / Eckstein, ...Authors: Chow, J. / Kovacic, F. / Dall Antonia, Y. / Krauss, U. / Fersini, F. / Schmeisser, C. / Lauinger, B. / Bongen, P. / Pietruszka, J. / Schmidt, M. / Menyes, I. / Bornscheuer, U.T. / Eckstein, M. / Thum, O. / Liese, A. / Mueller-Dieckmann, J. / Jaeger, K.E. / Streit, W.R.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LipS lipolytic enzyme
B: LipS lipolytic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6444
Polymers63,4852
Non-polymers1602
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-21 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.650, 170.650, 46.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-412-

HOH

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Components

#1: Protein LipS lipolytic enzyme


Mass: 31742.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: protein identified by using functional metagenomic screenings
Source: (gene. exp.) unidentified (others) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris, o.5% v/v Jeffamine ED-2001, 3.5 M NaBr, pH 8.5, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2011 / Details: Single Silicon (111) monochromator
RadiationMonochromator: Single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→46.3 Å / Num. all: 16386 / Num. obs: 15483 / % possible obs: 93.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2243 / % possible all: 95.9

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FBL,1TQH

4fbl

1tqh


Resolution: 2.8→46.3 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.836 / SU B: 16.578 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 2.915 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27022 833 5.1 %RANDOM
Rwork0.22262 ---
obs0.22512 15483 92.29 %-
all-16386 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2--0.53 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3779 0 2 37 3818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223874
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9745279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2315501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56223.425146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.17315614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6461524
X-RAY DIFFRACTIONr_chiral_restr0.10.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212920
X-RAY DIFFRACTIONr_mcbond_it0.7031.52507
X-RAY DIFFRACTIONr_mcangle_it1.34524022
X-RAY DIFFRACTIONr_scbond_it1.80331367
X-RAY DIFFRACTIONr_scangle_it3.164.51257
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 76 -
Rwork0.301 1143 -
obs--95.01 %

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